Dietary composition is a major driver of the ruminal and intestinal microbiomes in dairy cows and is implicated in digestive disorders such as subacute ruminal acidosis (SARA), which can be triggered by high-concentrate diets. Here, we used a longitudinal shotgun metagenomic approach to investigate the dynamics of ruminal and fecal microbiomes in seven dairy cows subjected to a controlled bidirectional dietary transition from low- to high-concentrate diets and back over two months. Samples were collected at three key stages of dietary modulation, enabling the assessment of temporal changes in microbial composition and function in relation to diet-associated physiological fluctuations. Shotgun metagenomic sequencing enabled a comprehensive characterization of community structure and functional potential across compartments and time, revealing a strong location effect with clear segregation between ruminal and fecal microbiomes, as well as diet-associated differences in diversity and composition. Our results highlight how gradual dietary concentrate transitions induce coordinated taxonomic and functional remodelling of the digestive microbiome in dairy cows and suggest that these responses may not be fully reversible over the course of a short experimental time frame.

Rumen microorganisms are primarily essential for feed decomposition and nutrition of the host animal, playing a key role in the health and well-being of cattle as well as the efficiency of milk or meat production. However, they also generate pollutant emissions such as methane. Analysing this microbiota under different farming conditions is therefore essential for optimizing production while minimizing its environmental impact. In this study, with metataxonomic sequencing and qPCR, we analysed the composition of the cow rumen microbiota sampled through the cannula and via esophageal tubing before morning feeding under two contrasting diets, low- and high-starch contents. Buccal swabs were also collected at the same sampling times to assess their potential as a proxy for the rumen microbiota. The two rumen sampling methods resulted in similar taxonomic compositions of bacteria, Archaea, fungi and protozoa and showed similar changes after the diet shift, indicating that the use of esophageal tubing is a reliable method for capturing the microbiota structure and its potential shifts following dietary changes. In contrast, the buccal swabs did not accurately reflect the rumen microbiota under the low- and high-starch diets, even after specific stringent filtering of the buccal sequences. Furthermore, we identified microbial markers of acidogenic challenge, with Dialister spp. also detected in buccal swab samples as potential indicators.

Microbes inhabiting the rumen convert fibrous plant material into usable energy for the host ruminant through a sophisticated network of microbial interactions. Metabolite crossfeeding is considered a key feature of the rumen microbiome, enhancing its stability, productivity, and efficiency in degrading plant material. This study analysed in vitro the metabolic interactions between two key rumen bacteria: the cellulolytic bacterium Fibrobacter succinogenes S85 and the saccharolytic bacterium Selenomonas ruminantium PC18. Additionally, the impact of Saccharomyces cerevisiae CNCM I-1077 on their metabolism and interactions was investigated. This strain is used as a feed additive for ruminants. Bacteria were cultured on either cellobiose or cellulose as carbon substrates. Interactions were studied through RNA-seq transcriptomic analysis of various microbial combinations, alongside substrate consumption and metabolite production measurements. The results revealed crossfeeding between F. succinogenes and S. ruminantium, as well as a significant upregulation of numerous F. succinogenes CAZyme genes in response to cellulose. The presence of the yeast strain under the different culture conditions induced metabolic and gene expression changes in both F. succinogenes and S. ruminantium. Notably, no lactate was detected when the yeast was added to S. ruminantium cultures or cocultures. Furthermore, the presence of bacteria influences yeast metabolism and crossfeeding between bacteria and yeast was suggested. The findings provide deeper insight into the in vitro interactions between F. succinogenes, S. ruminantium and S. cerevisiae, highlighting possible modes of action that may explain some of the observed positive effects of yeast on rumen function in vivo. This study underscores the mutual interactions between rumen bacteria and live yeast.

Probiotics are live yeast or bacterial organisms that have beneficial effects on the host. Several microorganisms exhibit probiotic properties, the most common types being lactic acid bacteria, Bifidobacteria, spore-forming bacteria, and some yeast strains. Saccharomyces cerevisiae var. boulardii is the most important probiotic yeast species. However, another group of foodborne microorganisms, the so-called non-Saccharomyces yeasts (NSYs), has recently been re-evaluated and shown to have enormous potential in various fields of application, ranging from food fermentation to human and animal applications. NSYs are able to produce a range of bioactive compounds such as antimicrobials, mannoproteins, enzymes, polyunsaturated fatty acids, essential amino acids, vitamins, and β-glucans, which increases their potential applications as a new class of probiotics and/or alternatives to antibiotics in animal husbandry. In this review, we aim to highlight the potential and benefits of NSYs as probiotics and natural antimicrobials to improve animal health. Furthermore, the use of NSYs as biological alternatives to antibiotics to control foodborne pathogens in animal production is discussed.

The honey bee Apis mellifera is exposed to a variety of biotic and abiotic stressors, such as the highly prevalent microsporidian parasite Nosema (Vairimorpha) ceranae and neonicotinoid insecticides. Both can affect honey bee physiology and microbial gut communities, eventually reducing its lifespan. They can also have a combined effect on the insect's survival. The use of bacterial probiotics has been proposed to improve honey bee health, but their beneficial effect remains an open question. In the present study, western honey bees were experimentally infected with N. ceranae spores, chronically exposed to the neonicotinoid thiamethoxam, and/or supplied daily with the homofermentative bacterium Pediococcus acidilactici MA18/5M thought to improve the honey bees' tolerance to the parasite. Deep shotgun metagenomic sequencing allowed the response of the gut microbiota to be investigated with a taxonomic resolution at the species level. All treatments induced significant changes in honey bee gut bacterial communities. Nosema ceranae infection increased the abundance of Proteus mirabilis, Frischella perrara, and Gilliamella apicola and reduced the abundance of Bifidobacterium asteroides, Fructobacillus fructosus, and Lactobacillus spp. Supplementation with P. acidilactici overturned some of these alterations, bringing back the abundance of some altered species close to the relative abundance found in the controls. Surprisingly, the exposure to thiamethoxam also restored the relative abundance of some species modulated by N. ceranae. This study shows that stressors and probiotics may have an antagonistic impact on honey bee gut bacterial communities and that P. acidilactici may have a protective effect against the dysbiosis induced by an infection with N. ceranae.

The supplementation of animal feed with microbial additives remains questioning for the traditional or quality label raw milk cheeses with regard to microbial transfer to milk. We evaluated the effect of dietary administration of live yeast on performance and microbiota of raw milk, teat skin, and bedding material of dairy cows. Two balanced groups of cows (21 primiparous 114 ± 24 DIM, 18 multiparous 115 ± 33 DIM) received either a concentrate supplemented with Saccharomyces cerevisiae CNCM I-1077 (1 × 1010 CFU/d) during four months (LY group) or no live yeast (C group). The microbiota in individual milk samples, teat skins, and bedding material were analysed using culture dependent techniques and high-throughput amplicon sequencing. The live yeast supplementation showed a numerical increase on body weight over the experiment and there was a tendency for higher milk yield for LY group. A sequence with 100% identity to that of the live yeast was sporadically found in fungal amplicon datasets of teat skin and bedding material but never detected in milk samples. The bedding material and teat skin from LY group presented a higher abundance of Pichia kudriavzevii reaching 53% (p < 0.05) and 10% (p < 0.05) respectively. A significant proportion of bacterial and fungal ASVs shared between the teat skin and the milk of the corresponding individual was highlighted.

We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3–5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity.

BACKGROUND:Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation, including microbiota colonization. This study evaluated the effect of rearing mode (mothered or artificially reared) on the establishment of the rumen and intestinal microbiome of lambs from birth to weaning. We also measured immunological and zootechnical parameters to assess lambs' growth and health. GIT anatomy as well as rumen and intestinal epithelium gene expression were also analysed on weaned animals to assess possible long-term effects of the rearing practice.RESULTS:Total VFA concentrations were higher in mothered lambs at 2 months of age, while artificially-reared lambs had lower average daily gain, a more degraded sanitary status and lower serum IgG concentration in the early growth phase. Metataxonomic analysis revealed higher richness of bacterial and eukaryote populations in mothered vs. artificially-reared lambs in both Rumen and Feces. Beta diversity analysis indicated an evolution of rumen and fecal bacterial communities in mothered lambs with age, not observed in artificially-reared lambs. Important functional microorganisms such as the cellulolytic bacterium Fibrobacter succinogenes and rumen protozoa did not establish correctly before weaning in artificially-reared lambs. Enterobacteriaceae and Escherichia coli were dominant in the fecal microbiota of mothered lambs, but main E. coli virulence genes were not found differential between the two groups, suggesting they are commensal bacteria which could exert a protective effect against pathogens. The fecal microbiota of artificially-reared lambs had a high proportion of lactic acid bacteria taxa. No difference was observed in mucosa gene expression in the two lamb groups after weaning.CONCLUSIONS:The rearing mode influences gastrointestinal microbiota and health-associated parameters in offspring in early life: rumen maturation was impaired in artificially-reared lambs which also presented altered sanitary status and higher risk of gut dysbiosis. The first month of age is thus a critical period where the gastrointestinal tract environment and microbiota are particularly unstable and special care should be taken in the management of artificially fed newborn ruminants.

Dietary fibers exhibit well-known beneficial effects on human health, but their anti-infectious properties against enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is a major food-borne pathogen that causes acute traveler’s diarrhea. Its virulence traits mainly rely on adhesion to an epithelial surface, mucus degradation, and the secretion of two enterotoxins associated with intestinal inflammation. With the increasing burden of antibiotic resistance worldwide, there is an imperious need to develop novel alternative strategies to control ETEC infections. This study aimed to investigate, using complementary in vitro approaches, the inhibitory potential of two dietary-fiber-containing products (a lentil extract and yeast cell walls) against the human ETEC reference strain H10407. We showed that the lentil extract decreased toxin production in a dose-dependent manner, reduced pro-inflammatory interleukin-8 production, and modulated mucus-related gene induction in ETEC-infected mucus-secreting intestinal cells. We also report that the yeast product reduced ETEC adhesion to mucin and Caco-2/HT29-MTX cells. Both fiber-containing products strengthened intestinal barrier function and modulated toxin-related gene expression. In a complex human gut microbial background, both products did not elicit a significant effect on ETEC colonization. These pioneering data demonstrate the promising role of dietary fibers in controlling different stages of the ETEC infection process.

Craniometric and stereotaxic data from rats of different sex, strain and weight were compared. It was found that stereotaxic atlases can be used with rats of different sex and strain provided that the weights of the rats conform to those used in the reference atlas. If rats of different weights are used, greater accuracy can be achieved if bregma is used as the reference point for work with rostral structures and the interaural line for work with caudal structures.

Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a broad range of various microorganisms, differing in each GIT segment, which are essential for efficient utilization of feed, especially to use nutrients that are not or little degraded by endogenous enzymes. In addition, like in other animal species, the GIT microbiota is in permanent interplay with the host's cells and is involved in a lot of functions among which inflammation, immune homeostasis, and energy metabolism. As for other animals and humans, the horse gut microbiome is sensitive to diet, especially consumption of starch, fiber, and fat. Age, breeds, stress during competitions, transportation, and exercise may also impact the microbiome. Because of its size and its complexity, the equine GIT microbiota is prone to perturbations caused by external or internal stressors that may result in digestive diseases like gastric ulcer, diarrhea, colic, or colitis, and that are thought to be linked with systemic diseases like laminitis, equine metabolic syndrome or obesity. Thus, in this review we aim at understanding the common core microbiome -in terms of structure and function- in each segment of the GIT, as well as identifying potential microbial biomarkers of health or disease which are crucial to anticipate putative perturbations, optimize global practices and develop adapted nutritional strategies and personalized nutrition.

Enterotoxigenic Escherichia coli (ETEC) is the main infectious agent responsible for piglet post-weaning diarrhea with high mortality rates. Antimicrobials represent the current principal strategy for treating ETEC infections in pig farms, but the occurrence of multi-resistant bacterial strains has considerably increased in the last decades. Thus, finding non-antibiotic alternatives becomes a real emergency. In this context, we investigated the effect of a live yeast strain, Saccharomyces cerevisiae var boulardii CNCM I-1079 (SB) in an in vitro model of the weaning piglet colon implemented with a mucus phase (MPigut-IVM) inoculated with ETEC and coupled with an intestinal porcine cell line IPI-2I. We showed that SB was able to modulate the in vitro microbiota through an increase in Bacteroidiaceae and a decrease in Prevotellaceae families. Effluents collected from the SB treated bioreactors were able to mitigate the expression level of genes encoding non-gel forming mucins, tight junction proteins, innate immune pathway, and pro-inflammatory response in IPI-2I cells. Furthermore, SB exerted a significant protective effect against ETEC adhesion on porcine IPEC-J2 intestinal cells in a dose-dependent manner and showed a positive effect on ETEC-challenged IPEC-J2 by lowering expression of genes involved in pro-inflammatory immune responses. Our results showed that the strain SB CNCM I-1079 could prevent microbiota dysbiosis associated with weaning and protect porcine enterocytes from ETEC infections by reducing bacterial adhesion and modulating the inflammatory response.

BACKGROUND:In ruminants, physiological and nutritional changes occur peripartum. We investigated if gastro-intestinal microbiota, rumen metabolism and antioxidant status were affected around parturition and what could be the impact of a daily supplementation of a live yeast additive in late gestating ewes.METHODS:Rumen, feces and blood samples were collected from 2 groups of 14 ewes one month and a few days before parturition, and 2 weeks postpartum.RESULTS:In the control ewes close to parturition, slight changes in the ruminal microbiota were observed, with a decrease in the concentration F. succinogenes and in the relative abundance of the Fibrobacteres phylum. Moreover, a decrease in the alpha-diversity of the bacterial community and a reduced relative abundance of the Fibrobacteres phylum were observed in their feces. Control ewes were prone to oxidative stress, as shown by an increase in malondialdehyde (MDA) concentration, a lower total antioxidant status, and higher glutathione peroxidase (GPx) activity in the blood. In the yeast supplemented ewes, most of the microbial changes observed in the control group were alleviated. An increase in GPx activity, and a significant decrease in MDA concentration were measured.CONCLUSIONS:The live yeast used in this study could stabilize gastro-intestinal microbiota and reduce oxidative stress close to parturition.

BACKGROUND The effect of live yeast Saccharomyces cerevisiae strain CNCM I-1077 (SC) on the ruminal degradability of different forages commonly found in dairy diets in South America was evaluated. We also assessed if SC supplementation interacts with forage group to affect ruminal fiber degradability. Four non-lactating rumen-cannulated Holstein cows were randomly assigned to two treatment sequences: Control-SC-Control or SC-Control-SC, in a switchback design, with three 30-day periods. Cows in the SC treatment were supplied with 1 x 10(10) colony-forming units of yeast daily via rumen cannula. In situ degradability of dry matter (DM) and neutral detergent fiber (aNDF) was measured in 15 forages collected in South America. Forages were assigned to one of three groups: corn silages; tropical grasses (sugarcane silages and tropical grass silages); and temperate grasses and alfalfa (oat silages, ryegrass silages, alfalfa silage, and alfalfa hay). RESULTS Cows supplemented with SC had higher (P = 0.05) counts of yeasts and lower (P = 0.03) concentration of lactate in rumen fluid. There was no interaction between forage group and yeast supplementation (P > 0.10) on in situ degradability. The SC increased DM (by 4.6%) and aNDF degradation (by 10.3%) at 24 h of incubation (P < 0.05). Metabolomics revealed that a chemical entity (C17H29N6O3, m/z 365.2284 [M + H](+)) from the family of lipids and related molecules was suppressed in the rumen fluid of cows supplemented with SC. CONCLUSION The SC supplementation improved DM and aNDF degradability regardless of the forage group. (c) 2021 Society of Chemical Industry.

Enterotoxigenic Escherichia coli (ETEC) is the principal pathogen responsible for post-weaning diarrhea in newly weaned piglets. Expansion of ETEC at weaning is thought to be the consequence of various stress factors such as transient anorexia, dietary change or increase in intestinal inflammation and permeability, but the exact mechanisms remain to be elucidated. As the use of animal experiments raise more and more ethical concerns, we used a recently developed in vitro model of piglet colonic microbiome and mucobiome, the MPigut-IVM, to evaluate the effects of a simulated weaning transition and pathogen challenge at weaning. Our data suggested that the tested factors impacted the composition and functionality of the MPigut-IVM microbiota. The simulation of weaning transition led to an increase in relative abundance of the Prevotellaceae family which was further promoted by the presence of the ETEC strain. In contrast, several beneficial families such as Bacteroidiaceae or Ruminococcaceae and gut health related short chain fatty acids like butyrate or acetate were reduced upon simulated weaning. Moreover, the incubation of MPigut-IVM filtrated effluents with porcine intestinal cell cultures showed that ETEC challenge in the in vitro model led to an increased expression of pro-inflammatory genes by the porcine cells. This study provides insights about the etiology of a dysbiotic microbiota in post-weaning piglets.